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User: doctor.dee005

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doctor.dee005 • 120
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Location:
Bioinformatics Center, Pune
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Posts by doctor.dee005

<prev • 47 results • page 1 of 5 • next >
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Suggestions for better and accurate tool for PanGenome analysis.
... I am doing pan genome analysis of multiple genera. I am searching a tool which will work on protein files (I have annotated proteins for each genome). I wanted to run [Roary][1], but it requires .gff files as well. Any suggestions are welcomed. [1]: https://github.com/sanger-pathogens/Roary/tre ...
genome gene pangenome sequencing written 3 hours ago by doctor.dee005 • 120
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Answer: A: download genbank sequences with exon sequences highlighted
... You can use efetch from ncbi-entrez-direct utilities. But first, you must have the accessions (with start and end of seuences which you want to extract). Make one file for this data and use following command in any script. efetch -db nuccore -id NG_007524.1 -format fasta -chr_start start -chr_stop ...
written 3 days ago by doctor.dee005 • 120
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Answer: A: Programmatically retrieve the length of a gene
... Use [seq_stat.py][1], it will give output as tab-separated file, containg header, count of each nucleotide and sequence length. If multifasta file is provided, it will print this statistics. The sequence length of each sequence will be in last column. [1]: https://github.com/drdee255/Python-code ...
written 3 days ago by doctor.dee005 • 120
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Answer: A: Extract Reverse Reads Based on Header Information of Forward Reads
... use [fastq-pair][1], it gives the only reads which are in forward and reverse files. So, rather than making forward.txt(headers), make forward.fastq(containg reads for which you want reverse reads to be extracted) and run the program. This will make four files in the directory: 1. forward.fastq.p ...
written 3 days ago by doctor.dee005 • 120
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Answer: A: Continuous mismatch at the end of the alignment, how to eliminate it?
... The trailing unaligned regions are results of global alignments. Use mafft --localpair (local alignment), in which trailing unialign regions from both the ends are not considered in order to maximiza alignment scores. ...
written 13 days ago by doctor.dee005 • 120
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Answer: A: Advice for trimming asymmetric adapters for paired end sequencing library
... You can use [trimmomatic][1] for this kind of trimming where you can include your adapters in their adapter library and perform trimming. [1]: http://www.usadellab.org/cms/?page=trimmomatic ...
written 14 days ago by doctor.dee005 • 120
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Answer: A: copy number variation
... Just map the known genes on processed reads and note down the number of times they aligned. Use appropriate alignmnet parameters. You can use bowtie aligner. At last you will have number of times each gene aligned in both samples. Relatively, you can conclude on gene copy number variation, provided ...
written 14 days ago by doctor.dee005 • 120
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Answer: A: How to create a list of the barcodes located in the read headers of demultiplexe
... I suppose your header are like this: @7001367R:585:HNHVHBCXY:1:1102:1267:2073 1:N:0:ATTACTCG+TATAGCCT where `HNHVHBCXY` is your barcodes. If your fastq files are in gzip format. Do following: zcat file.fastq.gz | awk 'NR%4==1' | cut -d ':' -f3 | uniq ...
written 14 days ago by doctor.dee005 • 120 • updated 14 days ago by finswimmer ♦ 4.4k
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Comment: C: how to merge multiple tab-delimitated files
... You can find two files [here][1]. The expected output file should be like this ---- kmers genome1 genome2 AAAAAAAAAA 2 4 AAAAAAAAAC 8 3 AAAAAAAAAG 2 2 AAAAAAAAAT 8 8 AAAAAAAACA 27 25 In this format I want to merge two files. [1]: https://drive.google.com/open?id=1p1 ...
written 17 days ago by doctor.dee005 • 120 • updated 16 days ago by zx8754 ♦ 4.8k
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(Closed) How to merge multiple tab-delimitated files
... I have several (about 40 files) tab-delimited files for each genome (having k-mer counts). The format is AAAAAAAAAA 2 AAAAAAAAAC 8 AAAAAAAAAG 2 AAAAAAAAAT 8 AAAAAAAACA 27 I want to merge them. My ultimate aim is to make dataset of kmers of each genome. I have used [KMC][1] to c ...
genome R tools python linux written 17 days ago by doctor.dee005 • 120 • updated 16 days ago by zx8754 ♦ 4.8k

Latest awards to doctor.dee005

Scholar 17 days ago, created an answer that has been accepted. For A: Extract specific fasta sequences from multiple multi-fasta files located in a di
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